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- PDB-8x28: Crystal structure of H5 hemagglutinin from human-infecting H5N8 i... -

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Basic information

Entry
Database: PDB / ID: 8x28
TitleCrystal structure of H5 hemagglutinin from human-infecting H5N8 influenza virus
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsJin, X.Y. / Han, P. / Song, H. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122040 China
CitationJournal: To Be Published
Title: Enhanced binding of Sialyl Lewis X to hemagglutinin contributes to H5N8 mammalian pathogenicity and infectivity
Authors: Jin, X. / Zhang, C. / Maio, A.D. / Shi, Y. / Qi, J. / Bi, Y. / Liu, Y. / Song, H. / Gao, G.F.
History
DepositionNov 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
B: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,22420
Polymers346,1286
Non-polymers3,09714
Water00
1
A: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,61210
Polymers173,0643
Non-polymers1,5487
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-30 kcal/mol
Surface area59640 Å2
MethodPISA
2
B: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,61210
Polymers173,0643
Non-polymers1,5487
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15310 Å2
ΔGint-34 kcal/mol
Surface area60190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.932, 267.380, 131.188
Angle α, β, γ (deg.)90.000, 99.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Hemagglutinin


Mass: 57687.926 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Baculovirus transfer vector pFASTBAC1 / References: UniProt: A0A8E4ZAK5
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 3 % dextran sulfate sodium salt, 0.1 M bicine pH 7.7, 18 % w/v PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.19→267.38 Å / Num. obs: 82156 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 63.58 Å2 / Rmerge(I) obs: 0.349 / Net I/σ(I): 5.2
Reflection shellResolution: 3.19→3.27 Å / Rmerge(I) obs: 1.999 / Num. unique obs: 6061

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→32.04 Å / SU ML: 0.5113 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2592 3937 2.43 %
Rwork0.2419 57953 -
obs0.2423 61890 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.43 Å2
Refinement stepCycle: LAST / Resolution: 3.19→32.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23329 0 196 0 23525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005424060
X-RAY DIFFRACTIONf_angle_d0.691132583
X-RAY DIFFRACTIONf_chiral_restr0.04813513
X-RAY DIFFRACTIONf_plane_restr0.00554249
X-RAY DIFFRACTIONf_dihedral_angle_d15.15598908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.230.38541400.36535527X-RAY DIFFRACTION99.16
3.23-3.270.38661390.355704X-RAY DIFFRACTION99.37
3.27-3.310.34991420.3415707X-RAY DIFFRACTION99.76
3.31-3.360.38211390.33995559X-RAY DIFFRACTION99.55
3.36-3.410.35191400.34035588X-RAY DIFFRACTION99.46
3.41-3.460.32311440.32955784X-RAY DIFFRACTION99.58
3.46-3.510.3251380.32095592X-RAY DIFFRACTION99.58
3.51-3.570.33081390.2995598X-RAY DIFFRACTION99.76
3.57-3.630.28441440.2855733X-RAY DIFFRACTION99.73
3.63-3.70.28431370.28655538X-RAY DIFFRACTION99.72
3.7-3.770.26631440.28385686X-RAY DIFFRACTION99.71
3.77-3.840.27341440.28485723X-RAY DIFFRACTION99.83
3.84-3.930.25171380.26285566X-RAY DIFFRACTION99.67
3.93-4.020.27581450.2375711X-RAY DIFFRACTION99.83
4.02-4.120.27291400.23875630X-RAY DIFFRACTION99.86
4.12-4.230.26821380.22765687X-RAY DIFFRACTION99.83
4.23-4.350.24411390.22395672X-RAY DIFFRACTION99.86
4.35-4.490.22231430.20215637X-RAY DIFFRACTION99.71
4.49-4.650.18871420.19335626X-RAY DIFFRACTION99.86
4.65-4.840.24611420.19835720X-RAY DIFFRACTION99.91
4.84-5.060.22031400.20795586X-RAY DIFFRACTION99.79
5.06-5.320.28581380.20645689X-RAY DIFFRACTION99.59
5.32-5.660.24561440.20795662X-RAY DIFFRACTION99.59
5.66-6.090.21691410.21915669X-RAY DIFFRACTION99.73
6.09-6.70.22351410.23165630X-RAY DIFFRACTION99.84
6.7-7.660.22961420.2185627X-RAY DIFFRACTION99.81
7.66-9.60.22141390.18795649X-RAY DIFFRACTION99.76
9.6-32.040.17661350.17365453X-RAY DIFFRACTION95.9

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